vcf-compare: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On CentOS possible default full paths are:

/usr/bin/vcf-compare - from package: vcftools

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/vcf-compare - from package: vcftools

You may install the required package with command apt-get install {package}

Error in other languages:
vcf-compare: bevel nie gevind nie
vcf-compare: comandă negăsită
vcf-compare: comando não encontrado
vcf-compare: commande introuvable
vcf-compare: command not found
vcf-compare: käsku ei ole
vcf-compare: không tìm thấy lệnh
vcf-compare: komanda nerasta
vcf-compare: Kommando nicht gefunden.
vcf-compare: kommandot finns inte
vcf-compare: komut yok
vcf-compare: nie znaleziono polecenia
vcf-compare: níor aimsíodh an t-ordú
vcf-compare: no se encontró la orden
vcf-compare: no s'ha trobat l'ordre
vcf-compare: opdracht niet gevonden
vcf-compare: parancs nem található
vcf-compare: perintah tidak ditemukan
vcf-compare: príkaz nenájdený
vcf-compare: příkaz nenalezen
vcf-compare: команда не найдена
vcf-compare: командата не е открита
vcf-compare: 命令找不到
vcf-compare: コマンドが見つかりません